Contacts of the helix formed by residues 34 - 41 (chain C) in PDB entry 3MI9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN* 3.7 17.5 - - - +
1C MET* 3.6 14.3 - - - +
18C PRO* 4.2 13.5 - - + -
22C CYS* 3.7 1.8 - - - -
32C PHE 3.2 0.8 - - - -
33C HIS* 1.3 82.7 - - - +
35C GLN* 1.3 67.8 + - - +
36C VAL* 3.1 16.9 + - - -
37C CYS* 3.1 14.4 + - - +
38C PHE* 2.9 22.7 + - - +
87C ZN 2.3 33.6 - - - -
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 3.4 39.0 - - + +
50B GLN* 4.0 1.7 + - - +
56B GLN* 5.3 0.4 - - - +
176B PHE* 3.1 30.1 - - - -
179B THR* 3.6 15.5 - - + +
180B ASN* 2.9 22.6 + - - -
183B HIS* 3.5 21.0 - - + +
1C MET* 4.0 19.9 - - + +
34C CYS* 1.3 74.7 - - - +
36C VAL* 1.3 56.9 + - - +
38C PHE* 3.4 1.2 + - - +
39C ILE* 2.9 57.4 + - - +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN* 4.2 17.0 - - - +
46B GLN* 3.8 21.1 - - + +
47B ASP* 3.9 28.9 - - + +
50B GLN* 3.1 35.7 - - - +
22C CYS* 5.3 3.6 - - - -
34C CYS* 3.1 7.3 - - - -
35C GLN* 1.3 73.2 - - - +
37C CYS* 1.3 59.5 + - - +
39C ILE* 3.4 0.7 + - - -
40C THR* 2.7 45.4 + - + +
47C TYR* 6.2 0.2 - - + -
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C CYS* 3.5 15.5 - - - -
30C CYS 3.5 17.0 - - - +
31C CYS 3.5 1.8 - - - -
33C HIS* 3.7 7.0 - - - +
34C CYS* 3.1 11.2 + - - +
36C VAL* 1.3 79.7 - - - +
38C PHE* 1.3 58.0 + - - +
40C THR* 3.7 5.4 - - - -
41C LYS* 2.8 61.8 + - + +
87C ZN 2.3 35.9 - - - -
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B PHE* 3.4 30.1 - + - -
177B MET* 6.4 0.2 - - - -
180B ASN* 3.5 27.4 - - - -
184B LEU* 5.2 0.9 - - + -
245B LEU* 5.1 6.7 - - + -
1C MET* 3.6 11.0 - - + -
31C CYS 2.9 15.8 + - - +
32C PHE* 4.0 29.2 - + - -
34C CYS 2.9 16.8 + - - +
35C GLN* 3.7 3.1 - - - +
37C CYS* 1.3 77.2 - - - +
39C ILE* 1.3 70.8 + - + +
42C ALA* 3.3 22.2 + - + +
43C LEU* 3.1 51.7 + - + +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN 5.2 0.7 - - - +
43B ASN* 3.5 34.5 - - + +
180B ASN* 4.0 4.5 - - - +
183B HIS* 4.0 14.6 - - + +
184B LEU* 3.9 26.0 - - + -
35C GLN* 2.9 47.8 + - + +
36C VAL* 3.9 2.7 - - - +
38C PHE* 1.3 85.6 - - + +
40C THR* 1.3 57.0 + - - +
43C LEU* 3.3 18.5 - - + +
44C GLY 3.4 0.3 + - - -
45C ILE* 3.0 36.7 + - + -
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Residues in contact with THR 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN* 3.5 24.2 - - - +
26C TYR* 5.0 3.7 + - - -
36C VAL* 2.7 32.8 + - + +
37C CYS* 3.5 5.5 + - - -
39C ILE* 1.3 76.8 - - - +
41C LYS* 1.3 71.1 + - - +
44C GLY* 3.0 23.9 - - - -
45C ILE 3.2 19.6 - - - +
46C SER* 5.0 4.9 - - - -
47C TYR* 6.0 1.3 - - + -
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ASN* 2.5 32.1 + - - -
23C THR* 2.9 36.4 + - - +
24C ASN* 4.4 6.5 - - - +
25C CYS 3.3 24.1 + - - +
26C TYR* 3.8 34.3 - - + +
30C CYS* 3.1 29.4 + - - +
31C CYS* 3.3 17.3 - - - -
33C HIS* 5.2 0.8 - - - +
37C CYS* 2.8 39.9 + - + +
40C THR* 1.3 78.1 + - - +
42C ALA* 1.3 55.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il